Off topic:extracting some information from cuffdiff output
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8.2 years ago
zizigolu ★ 4.3k

hi,

I have this file from cuffdiff

> head(mycounts[,1:14])

     test_id     gene_id      gene         locus sample_1 sample_2 status  value_1  value_2 log2.fold_change.  test_stat p_value  q_value
1 XLOC_000001 XLOC_000001    NAC001   1:3630-5899       C1       C2     OK  8.16533  8.82461         0.1120220  0.2496490 0.79700 0.999241
2 XLOC_000002 XLOC_000002      DCL1 1:23145-33153       C1       C2     OK 12.65950 15.12090         0.2563240  0.0853285 0.73045 0.999241
3 XLOC_000003 XLOC_000003 AT1G01073 1:44676-44787       C1       C2 NOTEST  0.00000  0.00000         0.0000000  0.0000000 1.00000 1.000000
4 XLOC_000004 XLOC_000004     IQD18 1:52091-54692       C1       C2     OK  2.98590  3.46625         0.2152080  0.3954010 0.68640 0.999241
5 XLOC_000005 XLOC_000005 AT1G01115 1:56623-56740       C1       C2 NOTEST  0.00000  0.00000         0.0000000  0.0000000 1.00000 1.000000
6 XLOC_000006 XLOC_000006      GIF2 1:72324-74737       C1       C2     OK 23.01450 21.96440        -0.0673764 -0.0884016 0.93085 0.999241
  significant
1          no
2          no
3          no
4          no
5          no
6          no

How I can extract columns 3 and 10 if only the column 14(significant) is yes and only between sample C1 and C2 because I have another samples in lower rows??

Thank you

myposts RNA-Seq R sequencing gene • 2.1k views
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